There is one other totally wild way to do download the programming into your hardware. It is filled with paradoxes and potential gotchas, but when set correctly, you won't have to reboot your computer to download your programming.
This alternative method is to run Windows 98 (or its version of DOS) inside a VMWare virtual machine running inside Windows XP. (Vista untested. Sorry.)
Don't even ask me how this manages to work, but it does. Somehow, even though Windows XP won't allow for the direct control of the keyboard port by the Thrustmaster programming software, that very same software running inside Windows 98 or DOS inside a virtual machine running inside XP can. I just did a whole bunch of testing this morning, and it definately works with the FLCS + WCS. It probably works for the other classic Thrustmaster hardware too.
Amazingly the VMWare software you need is totally free. Windows 98 SE, however, is not, but you probably have access to an old Windows 98 SE installation CD if you look around / ask around / Google around hard enough. You may even have one sitting in a box of stuff that came with your old PC.
Here's the procedure:
First, download and install VMWare Server, which is a totally free software package for emulating computers within Windows. I myself use VMWare Workstation, which is a commercial product I reviewed earlier this year for CPU Magazine. Everything I've read says that VMWare Server and VMWare Workstation should work the same way for this.
Secondly, create a new virtual machine in VMWare. Give it 1GB of hard drive space, but it will use less when finished. Tell it you'll be installing Windows 98. Insert your Windows 98 SE CD (and/or boot floppy, if necessary - you can make one from the Win98 CD) , and install Windows 98 SE, which takes an hour or so. Then install the VMWare tools into that Win98 virtual machine (hint: pull down the VM menu and choose "Install VMWare Tools.") Optionally, download and install Internet Explorer 6 from Microsoft's web site, then run WindowsUpdate to get the 25 (or so) patches that are available to Windows 98 as of late 2006.
Thirdly, download and install the DOS Thrustmaster software that corresponds to your hardware into Windows 98 (into C:\TM), as well as the Windows loaders that Bob Church created for either the F-16 FLCS or the F22-Pro. Optionally, download and install the Windows Thrustmaster software into Windows 98 also. (Hint: once you install the Windows loader, copy a shortcut of the EXE file to your Windows 98 desktop.)
Fourthly, to download your stick's programming in Windows 98, reboot and get to the Win98 desktop in the virtual machine. Open a File Explorer window. Drag and drop your programming file (a .B50 file for the FLCS) onto the desktop shortcut for the Windows loader (your corresponding .M50 file should be in the same directory as the .B50 file). The Windows loader opens. Follow the prompts, and after a few minutes, your stick is all programmed and ready to go. Don't touch any keyboard or mouse while this is going on!!! You may see your keyboard's NumLock, CapsLock, and ScrollLock lights blinking during programming - this is normal.
Alternatively, when booting Windows 98, hold down the left Control key, then choose option 6: "Boot to Safe Mode Command Prompt Only." This gets you a DOS C: prompt. Type "CD \TM" (without the quotes) and then "TM" (no quotes), and now you're in the good-old DOS Thrustmaster software. Download the file to the stick as normal. (Hint: if the programming is finished but the system is just sitting there apparently doing nothing, press any key on a connected USB keyboard or move your USB mouse slightly, and then you'll get a "All Finished" message.)